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{{f5samples
{{f5samples
|id=FF:11466-119B8
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|name=Smooth Muscle Cells - Uterine, donor3
|sample_id=11466
|rna_tube_id=119B8
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|sample_company=Promocell
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|sample_species=Human (Homo sapiens)
|sample_strain=
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|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=5.6
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000056,CL:0000144,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000220,CL:0000222,CL:0000255,CL:0000355,CL:0000393,CL:0000514,CL:0000548,CL:0000680,CL:0000723,CL:0002321,CL:0002371,CL:0002601
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|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11466-119B8
|is_a=EFO:0002091;;FF:0000002;;FF:0000185;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000185;;FF:0000210
|name=Smooth Muscle Cells - Uterine, donor3
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11927,LSID835,release010,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10002,,,
|rna_box=119
|rna_catalog_number=N/A
|rna_concentration=0.224
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.1
|rna_od260/280=2.08
|rna_position=B8
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=119B8
|rna_weight_ug=5.6
|sample_age=
|sample_cell_catalog=C-14059
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=smooth muscle cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Promocell
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11466
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=uterus
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}}
}}

Revision as of 14:55, 21 March 2012


Name:Smooth Muscle Cells - Uterine, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueuterus
dev stageNA
sexfemale
ageNA
cell typesmooth muscle cell
cell lineNA
companyPromocell
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
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C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11927

Jaspar motifP-value
MA0002.20.669
MA0003.10.369
MA0004.10.69
MA0006.10.49
MA0007.10.132
MA0009.10.662
MA0014.10.848
MA0017.10.796
MA0018.22.61324e-4
MA0019.10.631
MA0024.10.00155
MA0025.10.163
MA0027.10.495
MA0028.10.00209
MA0029.10.45
MA0030.10.136
MA0031.10.0457
MA0035.20.119
MA0038.10.0401
MA0039.20.259
MA0040.10.537
MA0041.10.514
MA0042.10.932
MA0043.10.00414
MA0046.10.975
MA0047.20.424
MA0048.10.17
MA0050.10.16
MA0051.10.3
MA0052.10.939
MA0055.10.0544
MA0057.10.0855
MA0058.10.562
MA0059.10.266
MA0060.10.00992
MA0061.10.9
MA0062.20.488
MA0065.20.847
MA0066.10.67
MA0067.10.236
MA0068.10.747
MA0069.10.0957
MA0070.10.549
MA0071.10.498
MA0072.10.888
MA0073.10.953
MA0074.10.588
MA0076.10.00492
MA0077.10.12
MA0078.10.153
MA0079.20.297
MA0080.21.60797e-7
MA0081.10.00597
MA0083.10.00531
MA0084.10.913
MA0087.10.543
MA0088.10.00474
MA0090.10.0645
MA0091.10.488
MA0092.10.464
MA0093.10.532
MA0099.26.25114e-9
MA0100.10.426
MA0101.10.0268
MA0102.20.0922
MA0103.10.00145
MA0104.20.995
MA0105.10.0332
MA0106.10.39
MA0107.10.0179
MA0108.20.00457
MA0111.10.172
MA0112.20.0302
MA0113.10.803
MA0114.10.961
MA0115.10.888
MA0116.10.117
MA0117.10.58
MA0119.10.348
MA0122.10.896
MA0124.10.939
MA0125.10.145
MA0131.10.8
MA0135.10.797
MA0136.17.40613e-4
MA0137.20.724
MA0138.20.691
MA0139.10.0459
MA0140.10.594
MA0141.10.386
MA0142.10.208
MA0143.10.223
MA0144.10.713
MA0145.10.0975
MA0146.10.215
MA0147.10.702
MA0148.10.334
MA0149.10.696
MA0150.10.0851
MA0152.10.0101
MA0153.10.789
MA0154.10.496
MA0155.10.353
MA0156.10.268
MA0157.10.0422
MA0159.10.394
MA0160.10.756
MA0162.10.115
MA0163.10.0422
MA0164.10.478
MA0258.10.694
MA0259.10.353



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11927

Novel motifP-value
10.486
100.139
1000.698
1010.681
1020.902
1030.51
1040.627
1050.356
1060.999
1070.156
1080.211
1090.0612
110.156
1109.92908e-4
1110.197
1120.742
1130.00287
1140.483
1150.914
1160.277
1170.0167
1180.582
1190.988
120.949
1200.116
1210.951
1220.432
1231.13479e-4
1240.893
1250.53
1260.452
1270.678
1280.761
1290.963
130.178
1300.00823
1310.902
1320.748
1330.336
1340.439
1350.72
1360.838
1370.464
1380.137
1390.00618
140.222
1400.114
1410.37
1420.356
1430.969
1440.418
1450.523
1460.397
1470.115
1480.875
1490.425
150.679
1500.448
1510.569
1520.495
1530.242
1540.214
1550.00326
1560.857
1570.41
1580.00134
1590.0379
160.083
1600.257
1610.518
1620.813
1630.82
1640.977
1650.773
1660.409
1670.454
1680.979
1690.0821
170.935
180.142
190.0876
20.555
200.612
210.596
220.122
230.407
240.113
250.221
260.276
270.438
280.205
290.169
30.38
300.278
310.711
320.349
330.326
340.49
350.86
360.378
370.0948
380.675
390.244
40.394
400.813
410.12
420.47
430.547
440.937
450.546
460.36
470.755
480.293
490.523
50.596
500.598
510.376
520.44
530.0268
540.912
550.897
560.704
570.473
580.533
590.399
60.302
600.618
610.957
620.873
630.968
640.539
650.578
660.0927
670.599
680.277
690.471
70.356
700.476
710.0735
720.917
730.218
740.473
750.151
760.232
770.153
780.167
790.743
80.408
800.415
810.766
820.405
830.295
840.754
850.145
860.54
870.0102
880.301
890.169
90.184
900.745
910.119
920.43
930.732
940.79
950.201
960.644
970.417
980.555
990.0164



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11927


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000514 (smooth muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002601 (uterine smooth muscle cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003100 (female organism)
0003104 (mesenchyme)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0004290 (dermomyotome)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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